Brain data
Contents
Brain data#
This section presents results of brain MRI data. Below are quantitative T1 values computed using the MP2RAGE and the MTsat methods. These values are averaged within the gray matter and white matter masks.
Gray matter qMRI#
Code imports#
# Python imports
from IPython.display import clear_output
from pathlib import Path
import numpy as np
import pandas as pd
# Import custom tools
from tools.data import Data
from tools.plot import Plot
Download data#
data_type = 'brain'
release_version = 'latest'
dataset = Data(data_type)
dataset.download(release_version)
Archive: neuromod-anat-brain-qmri.zip
inflating: data/brain/results-neuromod-anat-brain-qmri.csv
inflating: data/brain/._results-neuromod-anat-brain-qmri.csv
inflating: data/brain/report-neuromod-anat-brain.html
inflating: data/brain/._report-neuromod-anat-brain.html
inflating: data/brain/neuromod-anat-brain.nextflow.log
inflating: data/brain/history-neuromod-anat-brain
inflating: data/brain/._history-neuromod-anat-brain
inflating: data/brain/timeline-neuromod-anat-brain.html
inflating: data/brain/._timeline-neuromod-anat-brain.html
--2022-06-14 00:05:29-- https://github.com/courtois-neuromod/anat-processing/releases/download//r20210726/neuromod-anat-brain-qmri.zip
Resolving github.com (github.com)... 140.82.114.4
Connecting to github.com (github.com)|140.82.114.4|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://objects.githubusercontent.com/github-production-release-asset-2e65be/333825187/8209c733-4891-4342-8c30-ccd075b128f8?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20220614%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20220614T000529Z&X-Amz-Expires=300&X-Amz-Signature=38e0771be3fe06bb5f9987801b94c45c86e13df4246d2d5ecd716556fcf336b5&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=333825187&response-content-disposition=attachment%3B%20filename%3Dneuromod-anat-brain-qmri.zip&response-content-type=application%2Foctet-stream [following]
--2022-06-14 00:05:29-- https://objects.githubusercontent.com/github-production-release-asset-2e65be/333825187/8209c733-4891-4342-8c30-ccd075b128f8?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20220614%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20220614T000529Z&X-Amz-Expires=300&X-Amz-Signature=38e0771be3fe06bb5f9987801b94c45c86e13df4246d2d5ecd716556fcf336b5&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=333825187&response-content-disposition=attachment%3B%20filename%3Dneuromod-anat-brain-qmri.zip&response-content-type=application%2Foctet-stream
Resolving objects.githubusercontent.com (objects.githubusercontent.com)... 185.199.110.133, 185.199.109.133, 185.199.108.133, ...
Connecting to objects.githubusercontent.com (objects.githubusercontent.com)|185.199.110.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 939721 (918K) [application/octet-stream]
Saving to: ‘neuromod-anat-brain-qmri.zip’
0K .......... .......... .......... .......... .......... 5% 20.4M 0s
50K .......... .......... .......... .......... .......... 10% 99.6M 0s
100K .......... .......... .......... .......... .......... 16% 65.5M 0s
150K .......... .......... .......... .......... .......... 21% 138M 0s
200K .......... .......... .......... .......... .......... 27% 117M 0s
250K .......... .......... .......... .......... .......... 32% 124M 0s
300K .......... .......... .......... .......... .......... 38% 132M 0s
350K .......... .......... .......... .......... .......... 43% 115M 0s
400K .......... .......... .......... .......... .......... 49% 130M 0s
450K .......... .......... .......... .......... .......... 54% 142M 0s
500K .......... .......... .......... .......... .......... 59% 138M 0s
550K .......... .......... .......... .......... .......... 65% 136M 0s
600K .......... .......... .......... .......... .......... 70% 139M 0s
650K .......... .......... .......... .......... .......... 76% 141M 0s
700K .......... .......... .......... .......... .......... 81% 132M 0s
750K .......... .......... .......... .......... .......... 87% 118M 0s
800K .......... .......... .......... .......... .......... 92% 135M 0s
850K .......... .......... .......... .......... .......... 98% 140M 0s
900K .......... ....... 100% 101M=0.009s
2022-06-14 00:05:29 (95.5 MB/s) - ‘neuromod-anat-brain-qmri.zip’ saved [939721/939721]
Load data plot it#
dataset.load()
fig_gm = Plot(dataset, plot_name = 'brain-1')
fig_gm.title = 'Brain gray matter qMRI microstructure'
# If you're running this notebook in a Jupyter Notebook (eg, on MyBinder), change 'jupyter-book' to 'notebook'
fig_gm.display('jupyter-book', tissue = 'GM')
subject session acquisition metric unit label mean \
0 1 1 MP2RAGE T1map second GM 1.48850
1 1 1 MP2RAGE T1map second WM 0.94136
2 1 2 MP2RAGE T1map second GM 1.46510
3 1 2 MP2RAGE T1map second WM 0.94620
4 1 3 MP2RAGE T1map second GM 1.28500
.. ... ... ... ... ... ... ...
123 6 4 NaN MTRmap percent WM 53.09780
124 6 4 MTS MTsat arbitrary GM 8.51250
125 6 4 MTS MTsat arbitrary WM 8.55280
126 6 4 MTS T1map second GM 1.53840
127 6 4 MTS T1map second WM 1.01220
std median iqr ... q3 \
0 0.15877 1.48480 0.18402 ... 1.58070
1 0.17416 0.87470 0.11626 ... 0.95667
2 0.17762 1.47210 0.18738 ... 1.56700
3 0.18076 0.87387 0.12917 ... 0.96739
4 0.41732 1.41230 0.59626 ... 1.62630
.. ... ... ... ... ...
123 6.36400 54.32840 4.36430 ... 56.20390
124 199.60140 1.72020 0.88756 ... 2.24390
125 235.75970 4.07040 1.01800 ... 4.46410
126 2.03670 1.73570 1.29400 ... 2.10790
127 0.41837 1.03040 0.41547 ... 1.25520
map \
0 /Users/agah/Desktop/KuzuData/anat/derivatives/...
1 /Users/agah/Desktop/KuzuData/anat/derivatives/...
2 /Users/agah/Desktop/KuzuData/anat/derivatives/...
3 /Users/agah/Desktop/KuzuData/anat/derivatives/...
4 /Users/agah/Desktop/KuzuData/anat/derivatives/...
.. ...
123 /Users/agah/Desktop/KuzuData/anat/derivatives/...
124 /Users/agah/Desktop/KuzuData/anat/derivatives/...
125 /Users/agah/Desktop/KuzuData/anat/derivatives/...
126 /Users/agah/Desktop/KuzuData/anat/derivatives/...
127 /Users/agah/Desktop/KuzuData/anat/derivatives/...
mask software \
0 /Users/agah/Desktop/KuzuData/anat/derivatives/... qMRLab 2 5 0
1 /Users/agah/Desktop/KuzuData/anat/derivatives/... qMRLab 2 5 0
2 /Users/agah/Desktop/KuzuData/anat/derivatives/... qMRLab 2 5 0
3 /Users/agah/Desktop/KuzuData/anat/derivatives/... qMRLab 2 5 0
4 /Users/agah/Desktop/KuzuData/anat/derivatives/... qMRLab 2 5 0
.. ... ...
123 /Users/agah/Desktop/KuzuData/anat/derivatives/... qMRLab 2 5 0
124 /Users/agah/Desktop/KuzuData/anat/derivatives/... qMRLab 2 5 0
125 /Users/agah/Desktop/KuzuData/anat/derivatives/... qMRLab 2 5 0
126 /Users/agah/Desktop/KuzuData/anat/derivatives/... qMRLab 2 5 0
127 /Users/agah/Desktop/KuzuData/anat/derivatives/... qMRLab 2 5 0
date map_basedon \
0 2021-07-24 21:40:04 sub-01_ses-001_UNIT1.nii.gz
1 2021-07-24 21:40:04 sub-01_ses-001_UNIT1.nii.gz
2 2021-07-24 21:40:05 sub-01_ses-002_UNIT1.nii.gz
3 2021-07-24 21:40:05 sub-01_ses-002_UNIT1.nii.gz
4 2021-07-24 21:42:37 sub-01_ses-003_UNIT1.nii.gz
.. ... ...
123 2021-07-24 22:57:39 sub-06_ses-004_acq-MTon_MTS_aligned.nii.gz|sub...
124 2021-07-24 23:19:58 sub-06_ses-004_acq-MTon_MTS_aligned.nii.gz|sub...
125 2021-07-24 23:19:58 sub-06_ses-004_acq-MTon_MTS_aligned.nii.gz|sub...
126 2021-07-24 23:19:58 sub-06_ses-004_acq-MTon_MTS_aligned.nii.gz|sub...
127 2021-07-24 23:19:58 sub-06_ses-004_acq-MTon_MTS_aligned.nii.gz|sub...
runtime OS \
0 Octave 5.2.0 x86_64-pc-linux-gnu
1 Octave 5.2.0 x86_64-pc-linux-gnu
2 Octave 5.2.0 x86_64-pc-linux-gnu
3 Octave 5.2.0 x86_64-pc-linux-gnu
4 Octave 5.2.0 x86_64-pc-linux-gnu
.. ... ...
123 Octave 5.2.0 x86_64-pc-linux-gnu
124 Octave 5.2.0 x86_64-pc-linux-gnu
125 Octave 5.2.0 x86_64-pc-linux-gnu
126 Octave 5.2.0 x86_64-pc-linux-gnu
127 Octave 5.2.0 x86_64-pc-linux-gnu
map_reference data_type
0 https://doi.org/10.1016/j.neuroimage.2009.10.002 derivative
1 https://doi.org/10.1016/j.neuroimage.2009.10.002 derivative
2 https://doi.org/10.1016/j.neuroimage.2009.10.002 derivative
3 https://doi.org/10.1016/j.neuroimage.2009.10.002 derivative
4 https://doi.org/10.1016/j.neuroimage.2009.10.002 derivative
.. ... ...
123 NaN derivative
124 https://doi.org/10.1002/mrm.21732 derivative
125 https://doi.org/10.1002/mrm.21732 derivative
126 https://doi.org/10.1002/mrm.21732 derivative
127 https://doi.org/10.1002/mrm.21732 derivative
[128 rows x 23 columns]
White matter qMRI#
fig_wm = Plot(dataset, plot_name = 'brain-2')
fig_wm.title = 'Brain white matter qMRI microstructure'
# If you're running this notebook in a Jupyter Notebook (eg, on MyBinder), change 'jupyter-book' to 'notebook'
fig_wm.display('jupyter-book', tissue = 'WM')
subject session acquisition metric unit label mean \
0 1 1 MP2RAGE T1map second GM 1.48850
1 1 1 MP2RAGE T1map second WM 0.94136
2 1 2 MP2RAGE T1map second GM 1.46510
3 1 2 MP2RAGE T1map second WM 0.94620
4 1 3 MP2RAGE T1map second GM 1.28500
.. ... ... ... ... ... ... ...
123 6 4 NaN MTRmap percent WM 53.09780
124 6 4 MTS MTsat arbitrary GM 8.51250
125 6 4 MTS MTsat arbitrary WM 8.55280
126 6 4 MTS T1map second GM 1.53840
127 6 4 MTS T1map second WM 1.01220
std median iqr ... q3 \
0 0.15877 1.48480 0.18402 ... 1.58070
1 0.17416 0.87470 0.11626 ... 0.95667
2 0.17762 1.47210 0.18738 ... 1.56700
3 0.18076 0.87387 0.12917 ... 0.96739
4 0.41732 1.41230 0.59626 ... 1.62630
.. ... ... ... ... ...
123 6.36400 54.32840 4.36430 ... 56.20390
124 199.60140 1.72020 0.88756 ... 2.24390
125 235.75970 4.07040 1.01800 ... 4.46410
126 2.03670 1.73570 1.29400 ... 2.10790
127 0.41837 1.03040 0.41547 ... 1.25520
map \
0 /Users/agah/Desktop/KuzuData/anat/derivatives/...
1 /Users/agah/Desktop/KuzuData/anat/derivatives/...
2 /Users/agah/Desktop/KuzuData/anat/derivatives/...
3 /Users/agah/Desktop/KuzuData/anat/derivatives/...
4 /Users/agah/Desktop/KuzuData/anat/derivatives/...
.. ...
123 /Users/agah/Desktop/KuzuData/anat/derivatives/...
124 /Users/agah/Desktop/KuzuData/anat/derivatives/...
125 /Users/agah/Desktop/KuzuData/anat/derivatives/...
126 /Users/agah/Desktop/KuzuData/anat/derivatives/...
127 /Users/agah/Desktop/KuzuData/anat/derivatives/...
mask software \
0 /Users/agah/Desktop/KuzuData/anat/derivatives/... qMRLab 2 5 0
1 /Users/agah/Desktop/KuzuData/anat/derivatives/... qMRLab 2 5 0
2 /Users/agah/Desktop/KuzuData/anat/derivatives/... qMRLab 2 5 0
3 /Users/agah/Desktop/KuzuData/anat/derivatives/... qMRLab 2 5 0
4 /Users/agah/Desktop/KuzuData/anat/derivatives/... qMRLab 2 5 0
.. ... ...
123 /Users/agah/Desktop/KuzuData/anat/derivatives/... qMRLab 2 5 0
124 /Users/agah/Desktop/KuzuData/anat/derivatives/... qMRLab 2 5 0
125 /Users/agah/Desktop/KuzuData/anat/derivatives/... qMRLab 2 5 0
126 /Users/agah/Desktop/KuzuData/anat/derivatives/... qMRLab 2 5 0
127 /Users/agah/Desktop/KuzuData/anat/derivatives/... qMRLab 2 5 0
date map_basedon \
0 2021-07-24 21:40:04 sub-01_ses-001_UNIT1.nii.gz
1 2021-07-24 21:40:04 sub-01_ses-001_UNIT1.nii.gz
2 2021-07-24 21:40:05 sub-01_ses-002_UNIT1.nii.gz
3 2021-07-24 21:40:05 sub-01_ses-002_UNIT1.nii.gz
4 2021-07-24 21:42:37 sub-01_ses-003_UNIT1.nii.gz
.. ... ...
123 2021-07-24 22:57:39 sub-06_ses-004_acq-MTon_MTS_aligned.nii.gz|sub...
124 2021-07-24 23:19:58 sub-06_ses-004_acq-MTon_MTS_aligned.nii.gz|sub...
125 2021-07-24 23:19:58 sub-06_ses-004_acq-MTon_MTS_aligned.nii.gz|sub...
126 2021-07-24 23:19:58 sub-06_ses-004_acq-MTon_MTS_aligned.nii.gz|sub...
127 2021-07-24 23:19:58 sub-06_ses-004_acq-MTon_MTS_aligned.nii.gz|sub...
runtime OS \
0 Octave 5.2.0 x86_64-pc-linux-gnu
1 Octave 5.2.0 x86_64-pc-linux-gnu
2 Octave 5.2.0 x86_64-pc-linux-gnu
3 Octave 5.2.0 x86_64-pc-linux-gnu
4 Octave 5.2.0 x86_64-pc-linux-gnu
.. ... ...
123 Octave 5.2.0 x86_64-pc-linux-gnu
124 Octave 5.2.0 x86_64-pc-linux-gnu
125 Octave 5.2.0 x86_64-pc-linux-gnu
126 Octave 5.2.0 x86_64-pc-linux-gnu
127 Octave 5.2.0 x86_64-pc-linux-gnu
map_reference data_type
0 https://doi.org/10.1016/j.neuroimage.2009.10.002 derivative
1 https://doi.org/10.1016/j.neuroimage.2009.10.002 derivative
2 https://doi.org/10.1016/j.neuroimage.2009.10.002 derivative
3 https://doi.org/10.1016/j.neuroimage.2009.10.002 derivative
4 https://doi.org/10.1016/j.neuroimage.2009.10.002 derivative
.. ... ...
123 NaN derivative
124 https://doi.org/10.1002/mrm.21732 derivative
125 https://doi.org/10.1002/mrm.21732 derivative
126 https://doi.org/10.1002/mrm.21732 derivative
127 https://doi.org/10.1002/mrm.21732 derivative
[128 rows x 23 columns]